msa-parsers 5.3.0 → 5.4.1

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Files changed (30) hide show
  1. package/dist/gff/parseGFF.js +9 -1
  2. package/dist/gff/parseGFF.js.map +1 -1
  3. package/dist/index.d.ts +1 -1
  4. package/dist/msa/A3mMSA.js +8 -0
  5. package/dist/msa/A3mMSA.js.map +1 -1
  6. package/dist/msa/FastaMSA.d.ts +1 -0
  7. package/dist/msa/FastaMSA.js +7 -3
  8. package/dist/msa/FastaMSA.js.map +1 -1
  9. package/dist/msa/StockholmMSA.js +17 -3
  10. package/dist/msa/StockholmMSA.js.map +1 -1
  11. package/dist/msa/impgIntegration.test.d.ts +1 -0
  12. package/dist/msa/impgIntegration.test.js +49 -0
  13. package/dist/msa/impgIntegration.test.js.map +1 -0
  14. package/dist/msa/index.d.ts +2 -1
  15. package/dist/msa/index.js +20 -1
  16. package/dist/msa/index.js.map +1 -1
  17. package/dist/msa/index.test.js +28 -0
  18. package/dist/msa/index.test.js.map +1 -1
  19. package/dist/msa/stockholmParser.js +16 -30
  20. package/dist/msa/stockholmParser.js.map +1 -1
  21. package/package.json +2 -2
  22. package/src/gff/parseGFF.ts +9 -1
  23. package/src/index.ts +1 -1
  24. package/src/msa/A3mMSA.ts +9 -0
  25. package/src/msa/FastaMSA.ts +8 -3
  26. package/src/msa/StockholmMSA.ts +18 -4
  27. package/src/msa/impgIntegration.test.ts +57 -0
  28. package/src/msa/index.test.ts +32 -0
  29. package/src/msa/index.ts +26 -1
  30. package/src/msa/stockholmParser.ts +20 -30
package/dist/gff/parseGFF.js CHANGED
@@ -20,9 +20,17 @@ function parseAttributes(col9) {
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  const eq = f.indexOf('=');
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  const key = (eq === -1 ? f : f.slice(0, eq)).trim();
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  const val = eq === -1 ? undefined : f.slice(eq + 1);
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+ // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
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+ // literal comma encoded as %2C survives the split and isn't mistaken
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+ // for a separator
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  return [
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  key,
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- val ? safeDecode(val).trim().split(',').join(' ') : undefined,
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+ val
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+ ? val
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+ .split(',')
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+ .map(v => safeDecode(v).trim())
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+ .join(' ')
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+ : undefined,
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  ];
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  })
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  .filter(([key]) => key !== ''));
package/dist/gff/parseGFF.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,OAAO;YACL,GAAG;YACH,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS;SAC9D,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
1
+ {"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,wEAAwE;QACxE,qEAAqE;QACrE,kBAAkB;QAClB,OAAO;YACL,GAAG;YACH,GAAG;gBACD,CAAC,CAAC,GAAG;qBACA,KAAK,CAAC,GAAG,CAAC;qBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBAC9B,IAAI,CAAC,GAAG,CAAC;gBACd,CAAC,CAAC,SAAS;SACd,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
package/dist/index.d.ts CHANGED
@@ -1,5 +1,5 @@
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  export * from './types.ts';
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  export { generateNodeIds } from './util.ts';
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  export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.ts';
4
- export type { MSAParserType } from './msa/index.ts';
4
+ export type { MSAFormat, MSAParserType } from './msa/index.ts';
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  export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';
package/dist/msa/A3mMSA.js CHANGED
@@ -76,6 +76,14 @@ export default class A3mMSA extends BaseMSA {
76
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  if (seqs.length < 2) {
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  return false;
78
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  }
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+ // A true aligned FASTA (e.g. impg's fasta-aln output from soft-masked
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+ // references) has all rows the same total length. A3M's defining feature is
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+ // variable-length rows, since lowercase inserts live outside the fixed match
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+ // grid. So equal-length rows are an alignment, not A3M, even when lowercase
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+ // soft-masking is present.
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+ if (new Set(seqs.map(s => s.length)).size === 1) {
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+ return false;
86
+ }
79
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  let hasLowercase = false;
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  let firstMatchLen = -1;
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  let sameMatchLength = true;
package/dist/msa/A3mMSA.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/msa/FastaMSA.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import BaseMSA from './BaseMSA.ts';
2
2
  export default class FastaMSA extends BaseMSA {
3
3
  private MSA;
4
+ private orderedNames;
4
5
  constructor(text: string);
5
6
  getMSA(): {
6
7
  seqdata: Record<string, string>;
package/dist/msa/FastaMSA.js CHANGED
@@ -1,6 +1,9 @@
1
1
  import BaseMSA from "./BaseMSA.js";
2
2
  export default class FastaMSA extends BaseMSA {
3
3
  MSA;
4
+ // explicit insertion-ordered ids: object key order reorders integer-like
5
+ // keys (e.g. a numeric ">123" defline) to the front, scrambling row order
6
+ orderedNames = [];
4
7
  constructor(text) {
5
8
  super();
6
9
  const seqdata = {};
@@ -18,6 +21,7 @@ export default class FastaMSA extends BaseMSA {
18
21
  const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
19
22
  if (id) {
20
23
  seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
24
+ this.orderedNames.push(id);
21
25
  if (id.includes(':')) {
22
26
  colonNormalized[id.replaceAll(':', '_')] = id;
23
27
  }
@@ -29,7 +33,7 @@ export default class FastaMSA extends BaseMSA {
29
33
  return this.MSA;
30
34
  }
31
35
  getNames() {
32
- return Object.keys(this.MSA.seqdata);
36
+ return this.orderedNames;
33
37
  }
34
38
  getRow(name) {
35
39
  return (this.MSA.seqdata[name] ??
@@ -37,8 +41,8 @@ export default class FastaMSA extends BaseMSA {
37
41
  '');
38
42
  }
39
43
  getWidth() {
40
- const name = Object.keys(this.MSA.seqdata)[0];
41
- return this.getRow(name).length;
44
+ const name = this.orderedNames[0];
45
+ return name === undefined ? 0 : this.getRow(name).length;
42
46
  }
43
47
  }
44
48
  //# sourceMappingURL=FastaMSA.js.map
package/dist/msa/FastaMSA.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/msa/StockholmMSA.js CHANGED
@@ -9,7 +9,11 @@ export default class StockholmMSA extends BaseMSA {
9
9
  super();
10
10
  const res = parseAll(text);
11
11
  this.data = res;
12
- this.MSA = res[currentAlignment];
12
+ const aln = res[currentAlignment] ?? res[0];
13
+ if (!aln) {
14
+ throw new Error('No alignments found in Stockholm file');
15
+ }
16
+ this.MSA = aln;
13
17
  }
14
18
  getMSA() {
15
19
  return this.MSA;
@@ -19,7 +23,7 @@ export default class StockholmMSA extends BaseMSA {
19
23
  }
20
24
  getWidth() {
21
25
  const name = Object.keys(this.MSA.seqdata)[0];
22
- return this.getRow(name).length;
26
+ return name === undefined ? 0 : this.getRow(name).length;
23
27
  }
24
28
  get alignmentNames() {
25
29
  return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`);
@@ -85,9 +89,19 @@ export default class StockholmMSA extends BaseMSA {
85
89
  id: 'secondaryStruct',
86
90
  name: 'Secondary-structure',
87
91
  data: this.secondaryStructureConsensus,
92
+ // WUSS notation pairs base-paired columns as open/close brackets of
93
+ // several nesting types (<>, (), [], {}); color all opens one way and
94
+ // closes the other so every helix (e.g. the tRNA acceptor stem, which
95
+ // is written with parens) is highlighted, not just the <> arms.
88
96
  customColorScheme: {
89
- '>': 'pink',
90
97
  '<': 'lightblue',
98
+ '(': 'lightblue',
99
+ '[': 'lightblue',
100
+ '{': 'lightblue',
101
+ '>': 'pink',
102
+ ')': 'pink',
103
+ ']': 'pink',
104
+ '}': 'pink',
91
105
  },
92
106
  },
93
107
  ];
package/dist/msa/StockholmMSA.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/msa/impgIntegration.test.d.ts ADDED
@@ -0,0 +1 @@
1
+ export {};
package/dist/msa/impgIntegration.test.js ADDED
@@ -0,0 +1,49 @@
1
+ import { describe, expect, test } from 'vitest';
2
+ import A3mMSA from "./A3mMSA.js";
3
+ import FastaMSA from "./FastaMSA.js";
4
+ import { parseMSA } from "./index.js";
5
+ // impg (https://github.com/pangenome/impg) pipes `impg query -o fasta-aln` into
6
+ // scripts/faln2html.py, which feeds the FASTA string to
7
+ // MSAModelF().create({ data: { msa } }). These tests pin the behavior that
8
+ // integration relies on.
9
+ describe('impg fasta-aln integration', () => {
10
+ // PanSN-style names + region coordinates with colons, dash gaps, uppercase
11
+ const block = `>HG002#1#chr1:1000-1040
12
+ ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT
13
+ >HG003#1#chr1:1000-1040
14
+ ACGTAC-TGGACGTNNNNACGTAC--ACGTACGTACGT
15
+ >CHM13#0#chr1:1000-1040
16
+ ACGTACGTGGACGTNNNNACGT----ACGTACGTACGT`;
17
+ test('uppercase block is parsed as FASTA, not A3M/Clustal', () => {
18
+ const msa = parseMSA(block);
19
+ expect(msa).toBeInstanceOf(FastaMSA);
20
+ expect(msa.getNames()).toEqual([
21
+ 'HG002#1#chr1:1000-1040',
22
+ 'HG003#1#chr1:1000-1040',
23
+ 'CHM13#0#chr1:1000-1040',
24
+ ]);
25
+ expect(msa.getWidth()).toBe(38);
26
+ });
27
+ test('rows are retrievable by their colon-containing region name', () => {
28
+ const msa = parseMSA(block);
29
+ expect(msa.getRow('HG002#1#chr1:1000-1040')).toBe('ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT');
30
+ });
31
+ // If impg extracts from a soft-masked reference FASTA, aligned rows carry
32
+ // lowercase bases. A3M sniff runs before FASTA and triggers on
33
+ // hasLowercase && equal upper+dash match-length across rows -- which these
34
+ // rows satisfy by coincidence. The rows are all the same total length though,
35
+ // so they are a real alignment and must parse as FASTA, not A3M (A3M would
36
+ // strip the lowercase into separate insert columns and break alignment).
37
+ const softMasked = `>HG002#1#chr1:1000-1030
38
+ acgtACGTAC--GTACGTACGTACGTacgt
39
+ >HG003#1#chr1:1000-1030
40
+ ACGTacgtAC--GTACGTacgtACGTACGT`;
41
+ test('soft-masked equal-length block parses as FASTA, not A3M', () => {
42
+ const msa = parseMSA(softMasked);
43
+ expect(msa).toBeInstanceOf(FastaMSA);
44
+ expect(msa).not.toBeInstanceOf(A3mMSA);
45
+ const rows = msa.getNames().map(n => msa.getRow(n));
46
+ expect(new Set(rows.map(r => r.length)).size).toBe(1);
47
+ });
48
+ });
49
+ //# sourceMappingURL=impgIntegration.test.js.map
package/dist/msa/impgIntegration.test.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"impgIntegration.test.js","sourceRoot":"","sources":["../../src/msa/impgIntegration.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,gFAAgF;AAChF,wDAAwD;AACxD,2EAA2E;AAC3E,yBAAyB;AAEzB,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,2EAA2E;IAC3E,MAAM,KAAK,GAAG;;;;;uCAKuB,CAAA;IAErC,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC;YAC7B,wBAAwB;YACxB,wBAAwB;YACxB,wBAAwB;SACzB,CAAC,CAAA;QACF,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACjC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4DAA4D,EAAE,GAAG,EAAE;QACtE,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC3B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAC,IAAI,CAC/C,wCAAwC,CACzC,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,0EAA0E;IAC1E,+DAA+D;IAC/D,2EAA2E;IAC3E,8EAA8E;IAC9E,2EAA2E;IAC3E,yEAAyE;IACzE,MAAM,UAAU,GAAG;;;+BAGU,CAAA;IAE7B,IAAI,CAAC,yDAAyD,EAAE,GAAG,EAAE;QACnE,MAAM,GAAG,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;QAChC,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;QACnD,MAAM,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACvD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
package/dist/msa/index.d.ts CHANGED
@@ -6,7 +6,8 @@ import StockholmMSA from './StockholmMSA.ts';
6
6
  export { parseEmfTree } from 'emf-js';
7
7
  export { default as parseNewick } from './parseNewick.ts';
8
8
  export type MSAParserType = StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA;
9
- export declare function parseMSA(text: string, currentAlignment?: number): MSAParserType;
9
+ export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal';
10
+ export declare function parseMSA(text: string, currentAlignment?: number, format?: MSAFormat): MSAParserType;
10
11
  /**
11
12
  * Get ungapped sequence from an aligned row
12
13
  */
package/dist/msa/index.js CHANGED
@@ -5,7 +5,26 @@ import FastaMSA from "./FastaMSA.js";
5
5
  import StockholmMSA, { stockholmSniff } from "./StockholmMSA.js";
6
6
  export { parseEmfTree } from 'emf-js';
7
7
  export { default as parseNewick } from "./parseNewick.js";
8
- export function parseMSA(text, currentAlignment = 0) {
8
+ // when `format` is given the heuristic sniffing is bypassed -- callers that
9
+ // already know the format (e.g. impg emitting fasta-aln) can force it rather
10
+ // than rely on auto-detection, which is necessarily ambiguous between formats
11
+ // that share a leading '>' (fasta vs a3m)
12
+ export function parseMSA(text, currentAlignment = 0, format) {
13
+ if (format === 'stockholm') {
14
+ return new StockholmMSA(text, currentAlignment);
15
+ }
16
+ if (format === 'a3m') {
17
+ return new A3mMSA(text);
18
+ }
19
+ if (format === 'fasta') {
20
+ return new FastaMSA(text);
21
+ }
22
+ if (format === 'emf') {
23
+ return new EmfMSA(text);
24
+ }
25
+ if (format === 'clustal') {
26
+ return new ClustalMSA(text);
27
+ }
9
28
  if (stockholmSniff(text)) {
10
29
  return new StockholmMSA(text, currentAlignment);
11
30
  }
package/dist/msa/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/msa/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,YAAY,EAAE,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAEhE,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,kBAAkB,CAAA;AASzD,MAAM,UAAU,QAAQ,CAAC,IAAY,EAAE,gBAAgB,GAAG,CAAC;IACzD,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACvB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3B,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;AAC7B,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,UAAkB;IACpD,OAAO,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAA;AAC3C,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,iBAAiB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/msa/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,YAAY,EAAE,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAEhE,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAWzD,4EAA4E;AAC5E,6EAA6E;AAC7E,8EAA8E;AAC9E,0CAA0C;AAC1C,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,gBAAgB,GAAG,CAAC,EACpB,MAAkB;IAElB,IAAI,MAAM,KAAK,WAAW,EAAE,CAAC;QAC3B,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;IAC7B,CAAC;IACD,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACvB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3B,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;AAC7B,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,UAAkB;IACpD,OAAO,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAA;AAC3C,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,iBAAiB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA"}
package/dist/msa/index.test.js CHANGED
@@ -14,6 +14,18 @@ GHIKL`;
14
14
  expect(msa).toBeInstanceOf(FastaMSA);
15
15
  expect(msa.getNames()).toEqual(['seq1', 'seq2']);
16
16
  });
17
+ test('preserves row order for numeric FASTA ids', () => {
18
+ // object key order would hoist integer-like keys ('10' before '2'),
19
+ // scrambling the alignment; getNames must keep file order
20
+ const fasta = `>3
21
+ ACDEF
22
+ >1
23
+ GHIKL
24
+ >2
25
+ MNPQR`;
26
+ const msa = parseMSA(fasta);
27
+ expect(msa.getNames()).toEqual(['3', '1', '2']);
28
+ });
17
29
  test('parses A3M format', () => {
18
30
  const a3m = `>seq1
19
31
  ACDEFghiKLMNPQ
@@ -37,6 +49,22 @@ that doesn't match anything`;
37
49
  const msa = parseMSA(unknown);
38
50
  expect(msa).toBeInstanceOf(ClustalMSA);
39
51
  });
52
+ test('explicit format bypasses auto-detection', () => {
53
+ // a3m-looking input (lowercase inserts, differing row lengths) forced to
54
+ // FASTA, and FASTA-looking input forced to A3M
55
+ const a3mLooking = `>seq1
56
+ ACDEFghiKLMNPQ
57
+ >seq2
58
+ ACDEFKLMNPQ`;
59
+ expect(parseMSA(a3mLooking)).toBeInstanceOf(A3mMSA);
60
+ expect(parseMSA(a3mLooking, 0, 'fasta')).toBeInstanceOf(FastaMSA);
61
+ const fastaLooking = `>seq1
62
+ ACDEF
63
+ >seq2
64
+ GHIKL`;
65
+ expect(parseMSA(fastaLooking)).toBeInstanceOf(FastaMSA);
66
+ expect(parseMSA(fastaLooking, 0, 'a3m')).toBeInstanceOf(A3mMSA);
67
+ });
40
68
  });
41
69
  describe('FastaMSA colon-in-name lookup', () => {
42
70
  const fasta = `>EU105457.1|chr09:67680268..67675529_LTR/Copia
package/dist/msa/index.test.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.test.js","sourceRoot":"","sources":["../../src/msa/index.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,mBAAmB,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAC1D,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAE1C,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,KAAK,GAAG;;;MAGZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;;YAGJ,CAAA;QACR,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAEzB,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACpC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,OAAO,GAAG;;;;qBAIC,CAAA;QACjB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,OAAO,GAAG;4BACQ,CAAA;QACxB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,+BAA+B,EAAE,GAAG,EAAE;IAC7C,MAAM,KAAK,GAAG;;;WAGL,CAAA;IAET,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,iFAAiF,EAAE,GAAG,EAAE;QAC3F,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8EAA8E,EAAE,GAAG,EAAE;QACxF,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,sCAAsC,CAAC,CAAA;QAChE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,iCAAiC,EAAE,GAAG,EAAE;IAC/C,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,IAAI,GAAG,WAAW,CACtB,iEAAiE,CAClE,CAAA;QACD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,+CAA+C,CAAC,CAAA;IAC1E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,IAAI,GAAG,WAAW,CAAC,gCAAgC,CAAC,CAAA;QAC1D,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,IAAI,GAAG,WAAW,CAAC,sBAAsB,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,qBAAqB,EAAE,GAAG,EAAE;IACnC,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;QAC1B,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,cAAc,EAAE,GAAG,EAAE;QACxB,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oBAAoB,EAAE,GAAG,EAAE;QAC9B,MAAM,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,CAAC,mBAAmB,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
1
+ {"version":3,"file":"index.test.js","sourceRoot":"","sources":["../../src/msa/index.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,mBAAmB,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAC1D,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAE1C,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,KAAK,GAAG;;;MAGZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,2CAA2C,EAAE,GAAG,EAAE;QACrD,oEAAoE;QACpE,0DAA0D;QAC1D,MAAM,KAAK,GAAG;;;;;MAKZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IACjD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;;YAGJ,CAAA;QACR,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAEzB,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACpC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,OAAO,GAAG;;;;qBAIC,CAAA;QACjB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,OAAO,GAAG;4BACQ,CAAA;QACxB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,yCAAyC,EAAE,GAAG,EAAE;QACnD,yEAAyE;QACzE,+CAA+C;QAC/C,MAAM,UAAU,GAAG;;;YAGX,CAAA;QACR,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACnD,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QAEjE,MAAM,YAAY,GAAG;;;MAGnB,CAAA;QACF,MAAM,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACvD,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACjE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,+BAA+B,EAAE,GAAG,EAAE;IAC7C,MAAM,KAAK,GAAG;;;WAGL,CAAA;IAET,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,iFAAiF,EAAE,GAAG,EAAE;QAC3F,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8EAA8E,EAAE,GAAG,EAAE;QACxF,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,sCAAsC,CAAC,CAAA;QAChE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,iCAAiC,EAAE,GAAG,EAAE;IAC/C,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,IAAI,GAAG,WAAW,CACtB,iEAAiE,CAClE,CAAA;QACD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,+CAA+C,CAAC,CAAA;IAC1E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,IAAI,GAAG,WAAW,CAAC,gCAAgC,CAAC,CAAA;QAC1D,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,IAAI,GAAG,WAAW,CAAC,sBAAsB,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,qBAAqB,EAAE,GAAG,EAAE;IACnC,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;QAC1B,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,cAAc,EAAE,GAAG,EAAE;QACxB,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oBAAoB,EAAE,GAAG,EAAE;QAC9B,MAAM,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,CAAC,mBAAmB,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
package/dist/msa/stockholmParser.js CHANGED
@@ -13,6 +13,17 @@ function createStockholm() {
13
13
  seqdata: {},
14
14
  };
15
15
  }
16
+ // records before a "# STOCKHOLM 1.0" header are an error in strict mode,
17
+ // otherwise they implicitly start a new alignment
18
+ function ensureStock(stock, strict) {
19
+ if (stock) {
20
+ return stock;
21
+ }
22
+ if (strict) {
23
+ throw new Error('No format header: # STOCKHOLM 1.0');
24
+ }
25
+ return createStockholm();
26
+ }
16
27
  const formatStartRegex = /^# STOCKHOLM 1.0/;
17
28
  const formatEndRegex = /^\/\/\s*$/;
18
29
  const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/;
@@ -41,12 +52,7 @@ export function parseAll(text, opts) {
41
52
  stock = null;
42
53
  }
43
54
  else if ((match = gfRegex.exec(line))) {
44
- if (!stock) {
45
- if (options.strict) {
46
- throw new Error('No format header: # STOCKHOLM 1.0');
47
- }
48
- stock = createStockholm();
49
- }
55
+ stock = ensureStock(stock, !!options.strict);
50
56
  const tag = match[1];
51
57
  if (!stock.gf[tag]) {
52
58
  stock.gf[tag] = [];
@@ -54,12 +60,7 @@ export function parseAll(text, opts) {
54
60
  stock.gf[tag].push(match[2]);
55
61
  }
56
62
  else if ((match = gcRegex.exec(line))) {
57
- if (!stock) {
58
- if (options.strict) {
59
- throw new Error('No format header: # STOCKHOLM 1.0');
60
- }
61
- stock = createStockholm();
62
- }
63
+ stock = ensureStock(stock, !!options.strict);
63
64
  const tag = match[1];
64
65
  if (!stock.gc[tag]) {
65
66
  stock.gc[tag] = '';
@@ -67,12 +68,7 @@ export function parseAll(text, opts) {
67
68
  stock.gc[tag] += match[2];
68
69
  }
69
70
  else if ((match = gsRegex.exec(line))) {
70
- if (!stock) {
71
- if (options.strict) {
72
- throw new Error('No format header: # STOCKHOLM 1.0');
73
- }
74
- stock = createStockholm();
75
- }
71
+ stock = ensureStock(stock, !!options.strict);
76
72
  const seqname = match[1];
77
73
  const tag = match[2];
78
74
  const value = match[3];
@@ -85,12 +81,7 @@ export function parseAll(text, opts) {
85
81
  stock.gs[tag][seqname].push(value);
86
82
  }
87
83
  else if ((match = grRegex.exec(line))) {
88
- if (!stock) {
89
- if (options.strict) {
90
- throw new Error('No format header: # STOCKHOLM 1.0');
91
- }
92
- stock = createStockholm();
93
- }
84
+ stock = ensureStock(stock, !!options.strict);
94
85
  const seqname = match[1];
95
86
  const tag = match[2];
96
87
  const value = match[3];
@@ -103,12 +94,7 @@ export function parseAll(text, opts) {
103
94
  stock.gr[tag][seqname] += value;
104
95
  }
105
96
  else if ((match = lineRegex.exec(line))) {
106
- if (!stock) {
107
- if (options.strict) {
108
- throw new Error('No format header: # STOCKHOLM 1.0');
109
- }
110
- stock = createStockholm();
111
- }
97
+ stock = ensureStock(stock, !!options.strict);
112
98
  const seqname = match[1];
113
99
  const seqdata = match[2];
114
100
  if (!stock.seqdata[seqname]) {
package/dist/msa/stockholmParser.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,EAAE;KACZ,CAAA;AACH,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,SAAS,GAAG,uBAAuB,CAAA;AACzC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA4C;IAE5C,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IAEtC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;QAC3B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC/B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;QAC5B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,KAAK,CAAA;QACjC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA4C;IAE5C,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
1
+ {"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,EAAE;KACZ,CAAA;AACH,CAAC;AAED,yEAAyE;AACzE,kDAAkD;AAClD,SAAS,WAAW,CAClB,KAA2B,EAC3B,MAAe;IAEf,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAA;IACd,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;IACtD,CAAC;IACD,OAAO,eAAe,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,SAAS,GAAG,uBAAuB,CAAA;AACzC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA4C;IAE5C,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IAEtC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;QAC3B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC/B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;QAC5B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,KAAK,CAAA;QACjC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA4C;IAE5C,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "msa-parsers",
3
- "version": "5.3.0",
3
+ "version": "5.4.1",
4
4
  "license": "MIT",
5
5
  "type": "module",
6
6
  "repository": {
@@ -28,7 +28,7 @@
28
28
  },
29
29
  "devDependencies": {
30
30
  "typescript": "^6.0.3",
31
- "vitest": "^4.1.8"
31
+ "vitest": "^4.1.9"
32
32
  },
33
33
  "scripts": {
34
34
  "clean": "rimraf dist",
package/src/gff/parseGFF.ts CHANGED
@@ -23,9 +23,17 @@ function parseAttributes(col9?: string): Record<string, string | undefined> {
23
23
  const eq = f.indexOf('=')
24
24
  const key = (eq === -1 ? f : f.slice(0, eq)).trim()
25
25
  const val = eq === -1 ? undefined : f.slice(eq + 1)
26
+ // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
27
+ // literal comma encoded as %2C survives the split and isn't mistaken
28
+ // for a separator
26
29
  return [
27
30
  key,
28
- val ? safeDecode(val).trim().split(',').join(' ') : undefined,
31
+ val
32
+ ? val
33
+ .split(',')
34
+ .map(v => safeDecode(v).trim())
35
+ .join(' ')
36
+ : undefined,
29
37
  ]
30
38
  })
31
39
  .filter(([key]) => key !== ''),
package/src/index.ts CHANGED
@@ -17,7 +17,7 @@ export {
17
17
  parseNewick,
18
18
  stockholmSniff,
19
19
  } from './msa/index.ts'
20
- export type { MSAParserType } from './msa/index.ts'
20
+ export type { MSAFormat, MSAParserType } from './msa/index.ts'
21
21
 
22
22
  // GFF parsing
23
23
  export {
package/src/msa/A3mMSA.ts CHANGED
@@ -87,6 +87,15 @@ export default class A3mMSA extends BaseMSA {
87
87
  return false
88
88
  }
89
89
 
90
+ // A true aligned FASTA (e.g. impg's fasta-aln output from soft-masked
91
+ // references) has all rows the same total length. A3M's defining feature is
92
+ // variable-length rows, since lowercase inserts live outside the fixed match
93
+ // grid. So equal-length rows are an alignment, not A3M, even when lowercase
94
+ // soft-masking is present.
95
+ if (new Set(seqs.map(s => s.length)).size === 1) {
96
+ return false
97
+ }
98
+
90
99
  let hasLowercase = false
91
100
  let firstMatchLen = -1
92
101
  let sameMatchLength = true
package/src/msa/FastaMSA.ts CHANGED
@@ -6,6 +6,10 @@ export default class FastaMSA extends BaseMSA {
6
6
  colonNormalized: Record<string, string>
7
7
  }
8
8
 
9
+ // explicit insertion-ordered ids: object key order reorders integer-like
10
+ // keys (e.g. a numeric ">123" defline) to the front, scrambling row order
11
+ private orderedNames: string[] = []
12
+
9
13
  constructor(text: string) {
10
14
  super()
11
15
  const seqdata: Record<string, string> = {}
@@ -23,6 +27,7 @@ export default class FastaMSA extends BaseMSA {
23
27
  const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx)
24
28
  if (id) {
25
29
  seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '')
30
+ this.orderedNames.push(id)
26
31
  if (id.includes(':')) {
27
32
  colonNormalized[id.replaceAll(':', '_')] = id
28
33
  }
@@ -36,7 +41,7 @@ export default class FastaMSA extends BaseMSA {
36
41
  }
37
42
 
38
43
  getNames() {
39
- return Object.keys(this.MSA.seqdata)
44
+ return this.orderedNames
40
45
  }
41
46
 
42
47
  getRow(name: string) {
@@ -48,7 +53,7 @@ export default class FastaMSA extends BaseMSA {
48
53
  }
49
54
 
50
55
  getWidth() {
51
- const name = Object.keys(this.MSA.seqdata)[0]!
52
- return this.getRow(name).length
56
+ const name = this.orderedNames[0]
57
+ return name === undefined ? 0 : this.getRow(name).length
53
58
  }
54
59
  }
package/src/msa/StockholmMSA.ts CHANGED
@@ -14,7 +14,11 @@ export default class StockholmMSA extends BaseMSA {
14
14
  super()
15
15
  const res = parseAll(text)
16
16
  this.data = res
17
- this.MSA = res[currentAlignment]!
17
+ const aln = res[currentAlignment] ?? res[0]
18
+ if (!aln) {
19
+ throw new Error('No alignments found in Stockholm file')
20
+ }
21
+ this.MSA = aln
18
22
  }
19
23
 
20
24
  getMSA() {
@@ -26,8 +30,8 @@ export default class StockholmMSA extends BaseMSA {
26
30
  }
27
31
 
28
32
  getWidth() {
29
- const name = Object.keys(this.MSA.seqdata)[0]!
30
- return this.getRow(name).length
33
+ const name = Object.keys(this.MSA.seqdata)[0]
34
+ return name === undefined ? 0 : this.getRow(name).length
31
35
  }
32
36
 
33
37
  get alignmentNames() {
@@ -113,9 +117,19 @@ export default class StockholmMSA extends BaseMSA {
113
117
  id: 'secondaryStruct',
114
118
  name: 'Secondary-structure',
115
119
  data: this.secondaryStructureConsensus,
120
+ // WUSS notation pairs base-paired columns as open/close brackets of
121
+ // several nesting types (<>, (), [], {}); color all opens one way and
122
+ // closes the other so every helix (e.g. the tRNA acceptor stem, which
123
+ // is written with parens) is highlighted, not just the <> arms.
116
124
  customColorScheme: {
117
- '>': 'pink',
118
125
  '<': 'lightblue',
126
+ '(': 'lightblue',
127
+ '[': 'lightblue',
128
+ '{': 'lightblue',
129
+ '>': 'pink',
130
+ ')': 'pink',
131
+ ']': 'pink',
132
+ '}': 'pink',
119
133
  },
120
134
  },
121
135
  ]
package/src/msa/impgIntegration.test.ts ADDED
@@ -0,0 +1,57 @@
1
+ import { describe, expect, test } from 'vitest'
2
+
3
+ import A3mMSA from './A3mMSA.ts'
4
+ import FastaMSA from './FastaMSA.ts'
5
+ import { parseMSA } from './index.ts'
6
+
7
+ // impg (https://github.com/pangenome/impg) pipes `impg query -o fasta-aln` into
8
+ // scripts/faln2html.py, which feeds the FASTA string to
9
+ // MSAModelF().create({ data: { msa } }). These tests pin the behavior that
10
+ // integration relies on.
11
+
12
+ describe('impg fasta-aln integration', () => {
13
+ // PanSN-style names + region coordinates with colons, dash gaps, uppercase
14
+ const block = `>HG002#1#chr1:1000-1040
15
+ ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT
16
+ >HG003#1#chr1:1000-1040
17
+ ACGTAC-TGGACGTNNNNACGTAC--ACGTACGTACGT
18
+ >CHM13#0#chr1:1000-1040
19
+ ACGTACGTGGACGTNNNNACGT----ACGTACGTACGT`
20
+
21
+ test('uppercase block is parsed as FASTA, not A3M/Clustal', () => {
22
+ const msa = parseMSA(block)
23
+ expect(msa).toBeInstanceOf(FastaMSA)
24
+ expect(msa.getNames()).toEqual([
25
+ 'HG002#1#chr1:1000-1040',
26
+ 'HG003#1#chr1:1000-1040',
27
+ 'CHM13#0#chr1:1000-1040',
28
+ ])
29
+ expect(msa.getWidth()).toBe(38)
30
+ })
31
+
32
+ test('rows are retrievable by their colon-containing region name', () => {
33
+ const msa = parseMSA(block)
34
+ expect(msa.getRow('HG002#1#chr1:1000-1040')).toBe(
35
+ 'ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT',
36
+ )
37
+ })
38
+
39
+ // If impg extracts from a soft-masked reference FASTA, aligned rows carry
40
+ // lowercase bases. A3M sniff runs before FASTA and triggers on
41
+ // hasLowercase && equal upper+dash match-length across rows -- which these
42
+ // rows satisfy by coincidence. The rows are all the same total length though,
43
+ // so they are a real alignment and must parse as FASTA, not A3M (A3M would
44
+ // strip the lowercase into separate insert columns and break alignment).
45
+ const softMasked = `>HG002#1#chr1:1000-1030
46
+ acgtACGTAC--GTACGTACGTACGTacgt
47
+ >HG003#1#chr1:1000-1030
48
+ ACGTacgtAC--GTACGTacgtACGTACGT`
49
+
50
+ test('soft-masked equal-length block parses as FASTA, not A3M', () => {
51
+ const msa = parseMSA(softMasked)
52
+ expect(msa).toBeInstanceOf(FastaMSA)
53
+ expect(msa).not.toBeInstanceOf(A3mMSA)
54
+ const rows = msa.getNames().map(n => msa.getRow(n))
55
+ expect(new Set(rows.map(r => r.length)).size).toBe(1)
56
+ })
57
+ })
package/src/msa/index.test.ts CHANGED
@@ -18,6 +18,20 @@ GHIKL`
18
18
  expect(msa.getNames()).toEqual(['seq1', 'seq2'])
19
19
  })
20
20
 
21
+ test('preserves row order for numeric FASTA ids', () => {
22
+ // object key order would hoist integer-like keys ('10' before '2'),
23
+ // scrambling the alignment; getNames must keep file order
24
+ const fasta = `>3
25
+ ACDEF
26
+ >1
27
+ GHIKL
28
+ >2
29
+ MNPQR`
30
+ const msa = parseMSA(fasta)
31
+
32
+ expect(msa.getNames()).toEqual(['3', '1', '2'])
33
+ })
34
+
21
35
  test('parses A3M format', () => {
22
36
  const a3m = `>seq1
23
37
  ACDEFghiKLMNPQ
@@ -46,6 +60,24 @@ that doesn't match anything`
46
60
 
47
61
  expect(msa).toBeInstanceOf(ClustalMSA)
48
62
  })
63
+
64
+ test('explicit format bypasses auto-detection', () => {
65
+ // a3m-looking input (lowercase inserts, differing row lengths) forced to
66
+ // FASTA, and FASTA-looking input forced to A3M
67
+ const a3mLooking = `>seq1
68
+ ACDEFghiKLMNPQ
69
+ >seq2
70
+ ACDEFKLMNPQ`
71
+ expect(parseMSA(a3mLooking)).toBeInstanceOf(A3mMSA)
72
+ expect(parseMSA(a3mLooking, 0, 'fasta')).toBeInstanceOf(FastaMSA)
73
+
74
+ const fastaLooking = `>seq1
75
+ ACDEF
76
+ >seq2
77
+ GHIKL`
78
+ expect(parseMSA(fastaLooking)).toBeInstanceOf(FastaMSA)
79
+ expect(parseMSA(fastaLooking, 0, 'a3m')).toBeInstanceOf(A3mMSA)
80
+ })
49
81
  })
50
82
 
51
83
  describe('FastaMSA colon-in-name lookup', () => {
package/src/msa/index.ts CHANGED
@@ -14,7 +14,32 @@ export type MSAParserType =
14
14
  | EmfMSA
15
15
  | ClustalMSA
16
16
 
17
- export function parseMSA(text: string, currentAlignment = 0): MSAParserType {
17
+ export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'
18
+
19
+ // when `format` is given the heuristic sniffing is bypassed -- callers that
20
+ // already know the format (e.g. impg emitting fasta-aln) can force it rather
21
+ // than rely on auto-detection, which is necessarily ambiguous between formats
22
+ // that share a leading '>' (fasta vs a3m)
23
+ export function parseMSA(
24
+ text: string,
25
+ currentAlignment = 0,
26
+ format?: MSAFormat,
27
+ ): MSAParserType {
28
+ if (format === 'stockholm') {
29
+ return new StockholmMSA(text, currentAlignment)
30
+ }
31
+ if (format === 'a3m') {
32
+ return new A3mMSA(text)
33
+ }
34
+ if (format === 'fasta') {
35
+ return new FastaMSA(text)
36
+ }
37
+ if (format === 'emf') {
38
+ return new EmfMSA(text)
39
+ }
40
+ if (format === 'clustal') {
41
+ return new ClustalMSA(text)
42
+ }
18
43
  if (stockholmSniff(text)) {
19
44
  return new StockholmMSA(text, currentAlignment)
20
45
  }
package/src/msa/stockholmParser.ts CHANGED
@@ -24,6 +24,21 @@ function createStockholm(): StockholmData {
24
24
  }
25
25
  }
26
26
 
27
+ // records before a "# STOCKHOLM 1.0" header are an error in strict mode,
28
+ // otherwise they implicitly start a new alignment
29
+ function ensureStock(
30
+ stock: StockholmData | null,
31
+ strict: boolean,
32
+ ): StockholmData {
33
+ if (stock) {
34
+ return stock
35
+ }
36
+ if (strict) {
37
+ throw new Error('No format header: # STOCKHOLM 1.0')
38
+ }
39
+ return createStockholm()
40
+ }
41
+
27
42
  const formatStartRegex = /^# STOCKHOLM 1.0/
28
43
  const formatEndRegex = /^\/\/\s*$/
29
44
  const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/
@@ -57,36 +72,21 @@ export function parseAll(
57
72
  }
58
73
  stock = null
59
74
  } else if ((match = gfRegex.exec(line))) {
60
- if (!stock) {
61
- if (options.strict) {
62
- throw new Error('No format header: # STOCKHOLM 1.0')
63
- }
64
- stock = createStockholm()
65
- }
75
+ stock = ensureStock(stock, !!options.strict)
66
76
  const tag = match[1]!
67
77
  if (!stock.gf[tag]) {
68
78
  stock.gf[tag] = []
69
79
  }
70
80
  stock.gf[tag].push(match[2]!)
71
81
  } else if ((match = gcRegex.exec(line))) {
72
- if (!stock) {
73
- if (options.strict) {
74
- throw new Error('No format header: # STOCKHOLM 1.0')
75
- }
76
- stock = createStockholm()
77
- }
82
+ stock = ensureStock(stock, !!options.strict)
78
83
  const tag = match[1]!
79
84
  if (!stock.gc[tag]) {
80
85
  stock.gc[tag] = ''
81
86
  }
82
87
  stock.gc[tag] += match[2]!
83
88
  } else if ((match = gsRegex.exec(line))) {
84
- if (!stock) {
85
- if (options.strict) {
86
- throw new Error('No format header: # STOCKHOLM 1.0')
87
- }
88
- stock = createStockholm()
89
- }
89
+ stock = ensureStock(stock, !!options.strict)
90
90
  const seqname = match[1]!
91
91
  const tag = match[2]!
92
92
  const value = match[3]!
@@ -98,12 +98,7 @@ export function parseAll(
98
98
  }
99
99
  stock.gs[tag][seqname].push(value)
100
100
  } else if ((match = grRegex.exec(line))) {
101
- if (!stock) {
102
- if (options.strict) {
103
- throw new Error('No format header: # STOCKHOLM 1.0')
104
- }
105
- stock = createStockholm()
106
- }
101
+ stock = ensureStock(stock, !!options.strict)
107
102
  const seqname = match[1]!
108
103
  const tag = match[2]!
109
104
  const value = match[3]!
@@ -115,12 +110,7 @@ export function parseAll(
115
110
  }
116
111
  stock.gr[tag][seqname] += value
117
112
  } else if ((match = lineRegex.exec(line))) {
118
- if (!stock) {
119
- if (options.strict) {
120
- throw new Error('No format header: # STOCKHOLM 1.0')
121
- }
122
- stock = createStockholm()
123
- }
113
+ stock = ensureStock(stock, !!options.strict)
124
114
  const seqname = match[1]!
125
115
  const seqdata = match[2]!
126
116
  if (!stock.seqdata[seqname]) {